1491. Virome analysis of irrigation water sources provides extensive insights into the diversity and distribution of plant viruses in agroecosystemsOlivera Maksimović, Katarina Bačnik, Mark Paul Selda Rivarez, Ana Vučurović, Nataša Mehle, Maja Ravnikar, Ion Gutiérrez-Aguirre, Denis Kutnjak, 2024, izvirni znanstveni članek Povzetek: Plant viruses pose a significant threat to agriculture. Several are stable outside their hosts, can enter water bodies and remain infective for prolonged periods of time. Even though the quality of irrigation water is of increasing importance in the context of plant health, the presence of plant viruses in irrigation waters is understudied. In this study, we conducted a large-scale high-throughput sequencing (HTS)-based virome analysis of irrigation and surface water sources to obtain complete information about the abundance and diversity of plant viruses in such waters. We detected nucleic acids of plant viruses from 20 families, discovered several novel plant viruses from economically important taxa, like Tobamovirus and observed the influence of the water source on the present virome. By comparing viromes of water and surrounding plants, we observed presence of plant viruses in both compartments, especially in cases of large-scale outbreaks, such as that of tomato mosaic virus. Moreover, we demonstrated that water virome data can extensively inform us about the distribution and diversity of plant viruses for which only limited information is available from plants. Overall, the results of the study provided extensive insights into the virome of irrigation waters from the perspective of plant health. It also suggested that an HTS-based water virome surveillance system could be used to detect potential plant disease outbreaks and to survey the distribution and diversity of plant viruses in the ecosystem. Ključne besede: plant viruses, environmental water testing, high-throughput sequencing, agroecosystems, irrigation water, virome Objavljeno v DiRROS: 29.03.2024; Ogledov: 406; Prenosov: 190
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1492. Keep it simple : improving the ex situ culture of Cystoseira s.l. to restore macroalgal forestsAna Lokovšek, Valentina Pitacco, Domen Trkov, Leon Lojze Zamuda, Annalisa Falace, Martina Orlando-Bonaca, 2023, izvirni znanstveni članek Povzetek: Brown algae from genus Cystoseira s.l. form dense underwater forests that represent the most productive areas in the Mediterranean Sea. Due to the combined effects of global and local stressors such as climate change, urbanization, and herbivore outbreaks, there has been a severe decline in brown algal forests in the Mediterranean Sea. Natural recovery of depleted sites is unlikely due to the low dispersal capacity of these species, and efficient techniques to restore such habitats are needed. In this context, the aims of our study were (1) to improve and simplify the current ex situ laboratory protocol for the cultivation of Gongolaria barbata by testing the feasibility of some cost-effective and time-efficient techniques on two donor sites of G. barbata and (2) to evaluate the survival and growth of young thalli during the laboratory phase and during the most critical five months after out-planting. Specifically, the following ex situ cultivation methods were tested: (A) cultivation on clay tiles in mesocosms with culture water prepared by three different procedures (a) filtered seawater with a 0.22 μm filter membrane, (b) filtered seawater with a 0.7 μm filter membrane (GF), and (c) UV-sterilized water, and (B) cultivation on clay tiles in open laboratory systems. After two weeks, all thalli were fixed to plastic lantern net baskets suspended at a depth of 2 m in the coastal sea (hybrid method), and the algal success was monitored in relation to the different donor sites and cultivation protocol. The satisfactory results of this study indicate that UV-sterilized water is suitable for the cultivation of G. barbata in mesocosm, which significantly reduces the cost of the laboratory phase. This opens the possibility of numerous and frequent algal cultures during the reproductive period of the species. Additionally, if the young thalli remain in the lantern net baskets for an extended period of several months, they can grow significantly in the marine environment without being exposed to pressure from herbivorous fish. Ključne besede: gojenje ex situ, obnova habitata, izboljšanje metodologije, gozdički rjavih alg, ex situ cultivation, mesocosm, open system, method improvement, brown algal forests restoration Objavljeno v DiRROS: 29.03.2024; Ogledov: 376; Prenosov: 259
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1493. Increased diversity of citrus tristeza virus in EuropeJelena Zindović, Miroslav Čizmović, Ana Vučurović, Paolo Margaria, Dijana Škorić, 2023, izvirni znanstveni članek Povzetek: This study investigated the genetic diversity of citrus tristeza virus (CTV) isolates from Montenegro and Croatia, European countries with the northernmost citrus growing regions situated on the Eastern Adriatic coast. Fifteen complete or nearly complete CTV genomes were reconstructed from high-throughput sequencing of samples collected in distinct municipalities in Montenegro and Opuzen municipality in Croatia. Phylogenetic analyses assigned some of the sequences to VT and T30 strains, previously recorded in Europe, while remarkably other isolates were placed in S1 and RB groups, which have not been reported in Europe so far. In addition, a new phylogenetic lineage including only isolates from Montenegro was delineated and tentatively proposed as the MNE cluster. Recombination analysis revealed evidence of 11 recombination events in the sequences obtained in this study, between isolates of related strains, within isolates of the same strain, and between distant strains. These findings show that CTV diversity in Europe is higher than reported before and calls for the re-evaluation of management strategies. Ključne besede: complete genomes, genotyping, citrus tristeza virus, CTV, non-EU strain Objavljeno v DiRROS: 29.03.2024; Ogledov: 439; Prenosov: 182
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1494. Recovering high-quality bacterial genomes from cross-contaminated cultures : a case study of marine Vibrio campbelliiNeža Orel, Eduard Fadeev, Gerhard J. Herndl, Valentina Turk, Tinkara Tinta, 2024, izvirni znanstveni članek Povzetek: Background: Environmental monitoring of bacterial pathogens is critical for disease control in coastal marine ecosystems to maintain animal welfare and ecosystem function and to prevent significant economic losses. This requires accurate taxonomic identification of environmental bacterial pathogens, which often cannot be achieved by commonly used genetic markers (e.g., 16S rRNA gene), and an understanding of their pathogenic potential based on the information encoded in their genomes. The decreasing costs of whole genome sequencing (WGS), combined with newly developed bioinformatics tools, now make it possible to unravel the full potential of environmental pathogens, beyond traditional microbiological approaches. However, obtaining a high-quality bacterial genome, requires initial cultivation in an axenic culture, which is a bottleneck in environmental microbiology due to cross-contamination in the laboratory or isolation of non-axenic strains. Results: We applied WGS to determine the pathogenic potential of two Vibrio isolates from coastal seawater. During the analysis, we identified cross-contamination of one of the isolates and decided to use this dataset to evaluate the possibility of bioinformatic contaminant removal and recovery of bacterial genomes from a contaminated culture. Despite the contamination, using an appropriate bioinformatics workflow, we were able to obtain high quality and highly identical genomes (Average Nucleotide Identity value 99.98%) of one of the Vibrio isolates from both the axenic and the contaminated culture. Using the assembled genome, we were able to determine that this isolate belongs to a sub-lineage of Vibrio campbellii associated with several diseases in marine organisms. We also found that the genome of the isolate contains a novel Vibrio plasmid associated with bacterial defense mechanisms and horizontal gene transfer, which may offer a competitive advantage to this putative pathogen. Conclusions: Our study shows that, using state-of-the-art bioinformatics tools and a sufficient sequencing effort, it is possible to obtain high quality genomes of the bacteria of interest and perform in-depth genomic analyses even in the case of a contaminated culture. With the new isolate and its complete genome, we are providing new insights into the genomic characteristics and functional potential of this sub-lineage of V. campbellii. The approach described here also highlights the possibility of recovering complete bacterial genomes in the case of non-axenic cultures or obligatory co-cultures. Ključne besede: whole-genome assembly, non-axenic culture, plasmid, marine bacteria, marine biology Objavljeno v DiRROS: 28.03.2024; Ogledov: 398; Prenosov: 223
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1500. Diketopyrrolopyrrole pigment core@multi-layer ▫$SiO_2$▫ shell with improved photochemical stabilityErika Švara Fabjan, Zineb Saghi, Paul A. Midgley, Mojca Otoničar, Goran Dražić, Miran Gaberšček, Andrijana Sever Škapin, 2018, izvirni znanstveni članek Povzetek: A model organic pigment (diketopyrrolopyrrole) is encapsulated by a silica coating in order to improve its photochemical stability. Unlike in previous works where single-layer silica coatings were used for similar purposes, we here propose creation of a multi-layer silica shell synthesized via in-situ sol-gel method, which should significantly improve the homogeneity and thus the protection ability of the coating. This is done by repeating the basic two-step process (pigment surface modification and silica encapsulation) several times, creating the final protective shell in a layer-by-layer fashion. The compositional and structural properties of the prepared coatings is studied using Fourier-transform infrared spectroscopy, differential thermal and thermogravimetric analysis, nitrogen adsorption measurements and transmission electron microscopy. Photochemical stability of non-encapsulated and encapsulated pigment particles is evaluated via the so-called fast-irradiation method. Various correlations between the essential coating properties, such as thickness, porosity, SiO2 content, and the corresponding photochemical stability of the samples are established and discussed in detail. As a whole, our results confirm the basic hypothesis, that multiple-layered silica shells show improved pigment protection ability in comparison to the single-layer coatings. Ključne besede: organic pigments, silica coating, encapsulation, morphology, photocemical stability Objavljeno v DiRROS: 27.03.2024; Ogledov: 450; Prenosov: 179
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